EcoMiD is a community-based birth cohort study designed to examine interactions between the gut microbiome conditions and enteric infections. We enrolled over 360 newborn infants from 10 communities along a rural-urban gradient in northwestern Ecuador to characterize enteropathogen infections and gut microbial communities in the children at multiple time points over their first two years of life. Specifically, we are interested in understanding 1) whether the gut microbiome characteristics are associated with differential responses to enteropathogen infections for acute and chronic child health outcomes; 2) how the gut microbiome responds to and recovers from enteric pathogen infection; and 3) whether the gut microbiome modifies the short and long-term health outcomes associated with enteric pathogen infections (i.e., diarrhea, EED, and child growth).